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User:Eric Martz/Sandbox 13

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Sequence Alignment Tools


Notes below were made in 2011. In 2016 I met my wishes by creating MSAReveal.Org. Please give it a try!


What I want:

  1.  % identity vs. length of each chain and number of identical residues/chain length for each chain
  2. colors that indicate identity/similarity/difference
  3. ability to block a region of the alignment and get identity and length for that region (could cut and paste a new job ...)


Contents

Uniprot.org

  • no % ident
  • gray colors


Jalview

Seems to be mostly an alignment editing tool.


ClustalW2 at EBI

ClustalW2

  • has colors but no color key
  • no % id (?!)
  • give a score but doesn't explain it.


RCSB Compare Structures

  • Smith-Waterman or Needleman-Wunsch does #1,#2 but only for sequences of 3D structures.
  • Smith-Waterman shows only the aligned segments, while Needleman-Wunsch shows full length with gaps.


Swiss-Model

Why doesn't it make a model of FlgE CamJe using 1wlg? 

>tr|Q83WM5|Q83WM5_CAMJE FlgE OS=Campylobacter jejuni GN=flgE PE=4 SV=1
MMRSLWSGVSGLQAHQVAMDVEGNNISNVNTTGFKYSRADFGTMFSQTVKIATAPTDGRG
GSNPLQIGLGVSVSSTTRIHSQGSVQTTDKNTDVAINGDGFFMVSDDGGLTRYLTRSGDF
KLDAYGNFVNNAGFVVQGWNINWDTQSIDSSRTPQNIFIDPGMHIPAAKSTEVAIKANLN
SGLSVGTAKTPIYGLDSVHGFNKKDGTAKNENDTGITQFYTTSKNSVEVTEKGVDCAALF
NGKGDGLNLRDGQGIWVSYADSKFSTDVPNGVNVFNPNTQATQNGVIFWGDENNAVNLDI
TLNGVRIQNNSIKSLDQAIEYINTFTAPTDTREGTGVKAVRKADGSGIEFINTNADGTTD
NMKNIDLVVNQANTAGERHNLTWQANNNSFQATSRKQGANSVWIPGNNPVNGTERIQIVT
AHKYVYSSTPVQLDPMYNPDGGPAFNQANINTPGTAENNYRNAVNGSLLNTTVRTFRTTE
DLRELLQRDARYGVDYDGSGGFEADGSDVNEGVKVTVGATGEFIISNPNVQSTPPNGIVQ
NNRRPHDISFNVTAYTDAKGKVSTNMAFTNIFKGFDGVLTVGNSNRQSEQLFLSAFSAGL
EIYDSLGSKHTLEVQFVKQSTTQDGGNEWQMIIRVPEPAEINTTGEGPNNIIVGTARFNN
DGSLANYSPKTINFSPNNGAAPNQQIKLSFGTSGSNDGLVSSNSASTLTGQATDGYTSGN
LKPDAIRVDDKGNILGEFTNGKTFAVAKMAMASVANNSGLEEIGGNLFKVTANSGAIVVG
EAGTGGRGEMKTSALEMSNVDLSRSLTELIIIQRGYQANSKTISTSDQMLQTLIQLKQ
>sp|P0A1J1|FLGE_SALTY Flagellar hook protein flgE OS=Salmonella typhimurium GN=flgE PE=1 SV=2
MSFSQAVSGLNAAATNLDVIGNNIANSATYGFKSGTASFADMFAGSKVGLGVKVAGITQD
FTDGTTTNTGRGLDVAISQNGFFRLVDSNGSVFYSRNGQFKLDENRNLVNMQGMQLTGYP
ATGTPPTIQQGANPAPITIPNTLMAAKSTTTASMQINLNSTDPVPSKTPFSVSDADSYNK
KGTVTVYDSQGNAHDMNVYFVKTKDNEWAVYTHDSSDPAATAPTTASTTLKFNENGILES
GGTVNITTGTINGATAATFSLSFLNSMQQNTGANNIVATNQNGYKPGDLVSYQINNDGTV
VGNYSNEQEQVLGQIVLANFANNEGLASQGDNVWAATQASGVALLGTAGSGNFGKLTNGA
LEASNVDLSKELVNMIVAQRNYQSNAQTIKTQDQILNTLVNLR

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

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